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S-V issue.

Subject is specimens and the verb remain has to be plural. only C maintains the correct relationship.

E is fragment with no subject, no verb.
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+1 for C.

I think choice E contains the word "specimens" in the end.

"with it a cup-like apparatus and remaining in it all the specimens"

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gsd85
John Mercer Brooke created a sounding apparatus that is essentially a rod,
connected to a string, that strikes the sea floor,
causing the tension on the string to slack and a ball to fall to the ground;
the rod, released from its weight, is easily drawn up,
bringing with it a cup-like apparatus, in which was remaining all specimens
able to adhere, for an extended period of time, to a special glue lining the cup.

(A) with it a cup-like apparatus, in which was remaining the specimens
(B) a cup-like apparatus with it, and in which remaining specimens
(C) with it a cup-like apparatus, in which remain the specimens
(D) with it a cup-like apparatus in which remains specimens
(E) with it a cup-like apparatus and remaining in it all the

I eliminated A because of the "was remaining". since we have present simple in non-underlined portions, we don't need to use past simple.
B - uses comma+and, but doesn't have an active verb.
C - looks good
D - specimens is plural, but the verb remains is singular. out.
E - if we put this option in the sentence, it doesn't make much sense...
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gsd85
John Mercer Brooke created a sounding apparatus that is essentially a rod, connected to a string, that strikes the sea floor, causing the tension on the string to slack and a ball to fall to the ground; the rod, released from its weight, is easily drawn up, bringing with it a cup-like apparatus, in which was remaining all specimens able to adhere, for an extended period of time, to a special glue lining the cup.

(A) with it a cup-like apparatus, in which was remaining the specimens
(B) a cup-like apparatus with it, and in which remaining specimens
(C) with it a cup-like apparatus, in which remain the specimens
(D) with it a cup-like apparatus in which remains specimens
(E) with it a cup-like apparatus and remaining in it all the

Specimens -------> remain

Hence (C) is correct...
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John Mercer Brooke created a sounding apparatus that is essentially a rod,
connected to a string, that strikes the sea floor,
causing the tension on the string to slack and a ball to fall to the ground;
the rod, released from its weight, is easily drawn up,
bringing with it a cup-like apparatus, in which was remaining all specimens
able to adhere, for an extended period of time, to a special glue lining the cup.

(A) with it a cup-like apparatus, in which was remaining the specimens -First, "was remaining" is wrong tense because the statement is a fact and we use present tense to depict a fact. Second, S-V disagreement between "was" and "specimens".
(B) a cup-like apparatus with it, and in which remaining specimens -Positioning of "with it" is wrong. Second, we need simple present rather than present continuous. Third, this choice is a fragment.
(C) with it a cup-like apparatus, in which remain the specimens -Correct
(D) with it a cup-like apparatus in which remains specimens -S-V disagreement between "remains" and "specimens"
(E) with it a cup-like apparatus and remaining in it all the -Changes the meaning of original sentence
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To know which one between C and E is correct, ones must understand the meaning behind it.
Other options are all wrong.
B violates parallel.
D has S-V agreement error, A uses wrong tense.
Also, C is right b/c of the parallel with the phrase before ";"
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bringing with it a cup-like apparatus, in which remain the specimens
correct usage. specimens is plural and hence remain is correct. C is right
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